Biomedical subjects

Jun Yokoyama

Publications and source records attributed to Jun Yokoyama.

16 recordsLinked to original sources

PubMed2006

Intraspecific variation of flower colour and its distribution within a sea lavender, Limonium wrightii (Plumbaginaceae), in the northwestern Pacific Islands.

Differentiation of flower colour is thought to be one of the most important factors promoting plant speciation. We describe the intraspecific variation of flower colour and its distribution in Limonium wrightii. We conducted a survey on 36 islands in the northwestern Pacific and discriminated six morphs of flower colour variation. Two flower colour morphs, pink and yellow, were most frequently observed, and their geographical distributions were basically allopatric. These two morphs were in contact in a narrow zone on Okinoerabu Island, located in the middle region of the Ryukyu Archipelago. In addition, orange, white, and ivory flower morphs were also found in this zone. The geographical distribution of pink and yellow morphs showed a "leapfrog" pattern; the distribution of pink flowers was divided into two areas, intercalated by the distribution of the yellow flower morph. The orange morph may have resulted from hybridization between the pink and yellow flower morphs.

Biological Evolution↗

PubMed2006

Evaluation of morphological and molecular variation in Plantago asiatica var. densiuscula, with special reference to the systematic treatment of Plantago asiatica var. yakusimensis.

Morphological and molecular variations in Plantago asiatica L. var. densiuscula Pilg. were analyzed to evaluate the genetic basis for recognizing the dwarf variety P. asiatica var. yakusimensis (Masam.) Ohwi. Considerable variation in the leaf size of P. asiatica var. densiuscula was observed, and no morphological discontinuities were found between the dwarf types of P. asiatica var. densiuscula and P. asiatica var. yakusimensis. Morphological analysis of plants grown under standardized conditions revealed that both environmental plasticity and genetic differentiation contributed to the dwarfisms. Molecular phylogenetic analysis of rDNA internal transcribed spacer (ITS) regions and the SUC1 locus encoding a sucrose transporter revealed that P. asiatica var. yakusimensis was genetically unique although the differentiation level was low. From the above results, we concluded that P. asiatica var. yakusimensis should be reduced to a form of P. asiatica var. densiuscula. Furthermore, the geographic distribution of the SUC1 genotype suggested multiple origins of dwarves, and possible hypotheses for the origins of dwarves are discussed.

Base Sequence↗

PubMed2006

Leaf-shape variation of Paederia foetida in Japan: reexamination of the small, narrow leaf form from Miyajima Island.

Variations in Paederia foetida L. leaf shape were examined to evaluate the taxonomic validity of the small, narrow leaf form of P. foetida f. microphylla Honda from Miyajima Island, Honshu, Japan. There is considerable variation in P. foetida individuals in terms of leaf size and leaf index (leaf length:leaf width ratio). On Miyajima Island, some individuals have narrow leaves with a high leaf index value, a phenotype represented by the type specimen of P. foetida f. microphylla, and some do not. Given that the leaf size of individuals from Miyajima Island is smaller than that of individuals from other localities in Japan, and that the small leaf phenotype is stable even under cultivation, P. foetida f. microphylla is classified as the form having the smallest leaf size. Anatomical examination of leaf blades revealed that the large variation in leaf size was attributable to variation in the number of leaf cells but not to differences in cell size or cell shape. Based on these results, we discuss the endemism of P. foetida f. microphylla.

Ecosystem↗

PubMed2006

Spatiotemporal expression of duplicate AGAMOUS orthologues during floral development in Phalaenopsis.

The AGAMOUS (AG) family of MADS-box genes plays important roles in controlling the development of the reproductive organs of flowering plants. To understand the molecular mechanisms behind the floral development in the orchid, we isolated and characterized two AG-like genes from Phalaenopsis that we denoted PhalAG1 and PhalAG2. Phylogenetic analysis indicated that PhalAG1 and PhalAG2 fall into different phylogenetic positions in the AG gene family as they belong to the C- and D-lineages, respectively. Reverse transcription-polymerase chair reaction (RT-PCR) analyses showed that PhalAG1 and PhalAG2 transcripts were detected in flower buds but not in vegetative organs. Moreover, in situ hybridization experiments revealed that PhalAG1 and PhalAG2 hybridization signals were observed in the lip, column, and ovule during the floral development of Phalaenopsis, with little difference between the expression patterns of the two genes. These results suggest that both AG-like genes in Phalaenopsis act redundantly with each other in floral development.

Amino Acid Motifs↗

PubMed2006

Xtbx6r, a novel T-box gene expressed in the paraxial mesoderm, has anterior neural-inducing activity.

T-box proteins are important transcriptional regulators in animal development. We searched the Xenopus laevis expressed sequence tag (EST) database using zebrafish tbx24 (Ztbx24) as a query and found a sequence. We then obtained corresponding clones from a neurula cDNA library. This novel gene has a T-box showing 53% homology with Xenopus laevis tbx6 (Xtbx6) and 51% with Ztbx24 at the amino acid level and is relatively close to Xtbx6 indicated by alignment analysis. In situ hybridization showed that it is expressed in the paraxial mesoderm in the caudal region in a very similar manner to Xtbx6, with a slight difference in that the former is emphasized more dorsally and has a more restricted distribution along the antero-posterior axis. From these results we named this gene Xtbx6r (tbx6-related). Xtbx6r or Xtbx6r-EnR, when overexpressed in animal caps, induced anterior neural markers but not mesodermal markers. In contrast, Xtbx6r-VP16, Xtbx6 and Ztbx24 induced various mesodermal markers. These results indicate that Xtbx6r is a transcriptional repressor and has activity different from that of Xtbx6 or Ztbx24. Xtbx6r induced Otx2, XAG and Pax6 in animal caps. This activity differed from that of Xbra-EnR or Xtbx6-EnR, suggesting that some differences in biological activity exist among the tested repressor-type T-box genes. Depletion of Xtbx6r by antisense morpholino oligo produced curved embryos, but did not affect expressions of MyoD, Myf5, XWnt8 or thylacine2, nor inhibited muscle differentiation or segmentation. The results of knockdown and overexpression experiments suggest that Xtbx6r is involved in some morphogenesis in the paraxial mesoderm.

Amino Acid Sequence↗

PubMed2005

Characterization of TrcMADS1 gene of Trillium camtschatcense (Trilliaceae) reveals functional evolution of the SOC1/TM3-like gene family.

Plant MADS-box genes encode transcriptional regulators that are critical for a number of developmental processes, such as the establishment of floral organ identity, flowering time, and fruit development. It appears that the MADS-box gene family has undergone considerable gene duplication and divergence within various angiosperm lineages. SUPPRESSOR OF OVEREXPRESSION OF CONSTANS 1 (SOC1)/Tomato MADS-box gene 3 (TM3)-like genes are members of the MADS-box gene family and have undergone repeated duplication events. Here, we isolated and characterized the SOC1/TM3-like gene TrcMADS1 from Trillium camtschatcense (Trilliaceae) to infer the ancestral function of SOC1/TM3-like genes. The alignment of SOC1/TM3-like genes revealed the presence of a highly conserved region in the C-terminal of predicted protein sequences, designated the SOC1 motif. Phylogenetic analysis indicated that TrcMADS1 is at the basal position of the SOC1/TM3-like gene family. The TrcMADS1 mRNA was detected in both vegetative and reproductive organs by RT-PCR. Our results suggest that duplicated copies of SOC1/TM3-like gene evolved to become variously functionally specialized.

Amino Acid Sequence↗

PubMed2005

Molecular phylogeny and evolution of alcohol dehydrogenase (Adh) genes in legumes.

BACKGROUND: Nuclear genes determine the vast range of phenotypes that are responsible for the adaptive abilities of organisms in nature. Nevertheless, the evolutionary processes that generate the structures and functions of nuclear genes are only now be coming understood. The aim of our study is to isolate the alcohol dehydrogenase (Adh) genes in two distantly related legumes, and use these sequences to examine the molecular evolutionary history of this nuclear gene. RESULTS: We isolated the expressed Adh genes from two species of legumes, Sophora flavescens Ait. and Wisteria floribunda DC., by a RT-PCR based approach and found a new Adh locus in addition to homologues of the Adh genes found previously in legumes. To examine the evolution of these genes, we compared the species and gene trees and found gene duplication of the Adh loci in the legumes occurred as an ancient event. CONCLUSION: This is the first report revealing that some legume species have at least two Adh gene loci belonging to separate clades. Phylogenetic analyses suggest that these genes resulted from relatively ancient duplication events.

Alcohol Dehydrogenase↗

PubMed2005

Molecular identification of the mycorrhizal fungi of the epiparasitic plant Monotropastrum humile var. glaberrimum (Ericaceae).

Achlorophyllous monotropoid plants (Monotropoideae, Ericaceae) are epiparasites that obtain all of their carbon from their host plants via connections with mycorrhizal fungi. The mycorrhizal fungi of the epiparasitic monotropoid Monotropastrum humile var. glaberrima were identified based on mitochondrial, large ribosomal DNA sequences, and were compared with those of another variety, M. humile var. humile. The fungi that inhabit M. humile var. glaberrimum belong to the Thelephoraceae, whereas that of M. humile var. humile is a member of the Russulaceae. Two explanations are possible for this phenomenon: a misunderstanding of the taxonomic position of M. humile var. glaberrimum, or a change in the fungal partner within the Monotropastrum.

DNA, Fungal↗

PubMed2004

The differentiation of sepal and petal morphologies in Commelinaceae.

The morphological transition of the first whorl of tepals into sepals occurs frequently during the diversification of angiosperms. Such transitions may play important roles in pollination modes. The B class genes, APETALA3 (AP3) and PISTILLATA (PI) in Arabidopsis thaliana and GLOBOSA (GLO) and DEFICIENS (DEF) in Antirrhinum majus, are required for the development of petals in the second whorl, and its homologs have been isolated and characterized from various plants. A recent study on tulip, a monocotyledonous plant, indicates that the morphology of petaloid tepals in the first and second whorls is consistent with the expansion of B class gene expression. Here, we report five B class genes, TRGLOA, TRGLOB, CCGLO, TRDEF and CCDEF, isolated and characterized from two commelinaceous plants, Tradescantia reflexa and Commelina communis, with distinct sepal and petal morphologies in monocots. Northern blot analysis and gene-specific reverse transcription-polymerase chain reaction (RT-PCR) studies using dissected floral organs reveal a lack or low level of DEF-like gene expression in these commelinaceous species in the first whorl, in contrast to previous results. The expression data suggest that DEF-like gene expression in Commelinaceae correlates with the production of petaloid organs in the first whorl.

Amino Acid Sequence↗

PubMed2004

Geographical distribution of two haplotypes of chloroplast DNA in four oak species (Quercus) in Japan.

Chloroplast DNA polymorphism in four oak species (Quercus serrata, Q. mongolica var. crispula, Q. dentata and Q. aliena) was studied using collections from a total of 127 localities in Japan and South Korea on the basis of five intergenic spacers (trnD-trnT, trnT-trnL, rps14-psaB, trnS-trnT and trnQ-trnS). Although no variation existed in sequences among the four species, a single nucleotide (T/C) substitution in the trnQ-trnS intergenic spacer was found in all the four species, resulting in two haplotypes (T- and C-type). Phylogenetic analyses of the four species and related species showed that the C-type is derived and even likely of monophyletic origin, while the T-type is ancestral. Geographically, the T-type is widespread from South Korea to Japan, whereas the C-type is restricted to eastern Japan with rare exceptions. "Eastern Japan" approximately coincides with the distribution range of the boreal conifer forest during the last glacial maximum. Overall evidence suggests that the mutation from T- to C-type occurred in an individual of one of the four oak species and then was transferred to all the species by hybridization in eastern Japan, and that the Kanto District provided individuals with the C-type with a refugium during the last glacial maximum.

Base Sequence↗

PubMed2004

Molecular phylogeny of Vincetoxicum (Apocynaceae-Asclepiadoideae) based on the nucleotide sequences of cpDNA and nrDNA.

Molecular phylogenetic analyses of Vincetoxicum and Tylophora (Apocynaceae-Asclepiadoideae) were conducted based on the nucleotide sequences of cpDNA (two intergenic spacers of trnL (UAA)-trnF (GAA) and psbA-trnH and three introns, i.e., atpF, trnG (UCC) and trnL (UAA)), and nrDNA (ITS and ETS regions). Our phylogenetic analysis revealed two monophyletic groups; one consisted of seven taxa of Tylophora and Vincetoxicum inamoenum, Vincetoxicum magnificum and Vincetoxicum macrophyllum (Clade I) and the other consisted of 17 accessions of Vincetoxicum (Clade II). The monophyly of the genus Vincetoxicum was not supported. Although many nucleotide substitutions were observed in Clade I, the genetic differentiation within Clade II was small. Low genetic diversification but considerable morphological divergence suggests that the species in Clade II had undergone rapid diversification. Although most species in Clade I have tiny flowers, those in Clade II have larger and more nectariferous ones. Thus, we hypothesized that the rapid morphological radiation in Clade II may have been due to the gaining of floral characters such as large flowers and large amounts of nectar corresponding to diverse pollinators.

Adaptation, Biological↗

PubMed2003

Morphological and molecular variation in Mitchella undulata, with special reference to the systematic treatment of the dwarf form from Yakushima.

Morphological and molecular variation in Mitchella undulata Siebold et Zucc. was examined to evaluate the genetic basis for recognizing the dwarf variety, M. undulata var. minor Masamune. Considerable variation in leaf size in M. undulata, but no obvious morphological discontinuities, were found between the normal and dwarf varieties. Instead, a weak cline running from the Pacific Ocean to the Sea of Japan was found. Anatomical observations of leaf blades revealed that the large variation in leaf size can be attributed to variation in the number of leaf cells and not to differences in cell size. A molecular analysis based on sequences of rDNA internal transcribed spacer regions indicated that there were two major genotypes in M. undulata with minor variation in haplotypes resulting from additional substitutions or putative recombination. The dwarf form from Yakushima was neither genetically uniform nor apparently differentiated from other populations. From these results, we conclude that the dwarf form of M. undulata should be treated at the rank of forma.

Base Sequence↗

PubMed2003

Molecular evolution of cycloidea-like genes in Fabaceae.

The cycloidea (CYC) gene controls floral symmetry in snapdragon (Antirrhinum majus). We investigated the evolution of CYC-like genes in some species of legumes that have zygomorphic flowers. Two to four CYC-like genes were isolated from a single species. The results of NJ and ML analyses indicate that CYC-like genes in legumes group into two monophyletic clades; one group consists of eight CYC-like genes (Clade 1) and the other contains three CYC-like genes and TB1 of maize (Clade 2). These phylogenetic trees and the Shimodaira-Hasegawa test suggest that Clade 1 is a sister of the original CYC group (Clade 3). Moreover, the result of the GeneTree analysis showed that the CYC-like genes experienced repeated duplication events during the evolution of legumes. We herein speculate as to the role of CYC-like genes in legumes and discuss the evolutionary processes that these genes have undergone.

Amino Acid Sequence↗

PubMed2003

The evolution of extreme shell shape variation in the land snail Ainohelix editha: a phylogeny and hybrid zone analysis.

Ainohelix editha from Hokkaido, Japan, exhibit great geographical variation in their shell morphology. In particular, A. editha in two quite separate locations, Shimamaki and Samani, are striking because they are extremely flat and have a sharp keel, whereas at adjacent sites the shells are globular or depressed-globular. We used mitochondrial 16S rRNA and nuclear ITS-2 sequences to infer a phylogeny among 47 snails from 29 locations. Snails from the two keeled-flat populations clustered separately in the phylogeny, suggesting that this unusual shell form could have evolved independently. A morphological analysis of shells collected along a transect between keeled-flat and globular snail sites showed a cline for shell shape and the angle of the keel. Two different mtDNA lineages were found across the transect, with a cline for an ITS-2 single nucleotide polymorphism. Together, the results may suggest a lack of reproductive isolation between keeled-flat and globular snails, with possible introgression by hybridization.

Animals↗

PubMed2003

Hybridization and introgression between Callicarpa japonica and C. mollis (Verbenaceae) in central Japan, as inferred from nuclear and chloroplast DNA sequences.

Callicarpa x shirasawana is a natural hybrid between C. japonica and C. mollis, and has a morphology that is intermediate between those of the parent species. Characterization of natural Callicarpa populations in the Atsumi Peninsula of central Japan, which all three of the above species inhabit sympatrically, revealed hybrids with various morphologies. Molecular analysis revealed a high occurrence of introgression of the C. japonica genome into that of C. mollis. Moreover, all individuals examined with morphology similar to that of C. mollis had genetic traces of hybridization with C. japonica. Molecular analysis of individual C. mollis and C. japonica from five other areas of Japan showed that introgression of C. japonica into C. mollis occurs widely. Molecular data also strongly suggested that the previously recognized C. x shirasawana individuals with intermediate morphology are not F1 hybrids between C. japonica and C. mollis, but instead are progeny of C. x shirasawana backcrossed with C. japonica. Moreover, it was revealed that individuals with F1-type genotypes are indistinguishable morphologically from pure C. mollis. The results of the present study point to the need for re-evaluation of natural populations of C. mollis and C. x shirasawana.

Base Sequence↗

PubMed2002

Bilateral testicular tumors: a report of nine cases with long-term follow-up.

BACKGROUND: The incidence and clinical features of bilateral germ cell testicular tumor (GCTT) in the Japanese population are not fully characterized. We examined the incidence, clinical features, management and outcome, sexual status, hormonal environment, implication of androgen replacement, and human leukocyte antigen (HLA) typing of bilateral GCTT. METHODS: We treated nine consecutive patients with bilateral GCTT from 1980 through to 1999, and reviewed their hospital and clinic charts. Testosterone, luteinizing hormone, follicle stimulating hormone, dehydroepiandrosterone, and dehydroepiandrosterone-sulfate were measured in bilateral orchiectomized patients. Human leukocyte antigen typing was assessed with peripheral lymphocyte. RESULTS: The incidence of bilateral GCTT against the total number of patients with GCTT was 9/274 (3.3%). The median age of the first tumor was 29 (range 21-75) years. Three cases were synchronous and the remaining six cases were metachronous. In the case of metachronous tumor, the median interval between first and contralateral tumor was 8 (range 2-25) years. Standard treatment was defined as surveillance policy in stage I, chemotherapy for higher stages of non-seminoma, and radiotherapy for stage II seminoma. Human leukocyte antigen typing was examined for seven cases. Five cases were positive for HLA-A24. The incidence of HLA-A24 in bilateral GCTT was identical to that of the Japanese population. The relapsing incidence of stage I disease with surveillance policy was almost identical to unilateral GCTT. A 74-year-old patient with stage II seminoma died of the disease at 1.3 years. The other eight patients remained well without any evidence of recurrence at a median follow-up period of 78 (range 12-204) months. Four patients with bilateral orchiectomy did not require androgen replacement without easy fatigability. Sexual status was conserved using androgen replacement. CONCLUSIONS: Long-term follow-up, as long as 25 years, is recommended for contralateral relapse. Some patients with bilateral orchiectomy do not require androgen replacement. The significance of HLA-A24 for bilateral testicular tumor is equivocal in the Japanese population.

Adult↗